Nucmer manual

Code MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. Project Samples Project Activity See All Activity > Categories Bio-Informatics License Artistic License NucDiff manual. 1 Introduction. By default, NUCmer will be run with its default parameters values, except the --maxmatch parameter. --maxmatch is hard coded and cannot be changed. To change any other parameter values, type parameter names and new values inside single or double quotation marks. Nucmer can take very long to run in the presence of many repeats. Setting the -mum option can really speed things up, but some alignment information will be lost because -mum requires all match anchors to be unique. MUMmer User Manual. General Linux. To run this software interactively in a Linux environment run the command (s): module load mummer. mummer [options] input1.fasta input2.fasta > mummer.output. For a complete list of options, please visit the MUMmer homepage, or use the command: mummer -h. Other MUMmer programs may be found in the directory. nucmer -maxmatch CO92.fasta KIM.fasta-maxmatch Find maximal exact matches (MEMs) delta-filter -r -q out.delta > out.filter-r Filter out repetitive reference alignments-q Filter out repetitive query alignment show-snps -r -I -T -x 10 out.filter > out.snps-r Sort SNPs by reference position-I Do not output indels-T Tab delimited output Plug the tool in the tool_config.xml +of your galaxy instance and refresh the tools or restart the galaxy server. + + +# TESTING +You can test the code by running Nucmer on the test data and visualise the results in MUMmerplot. +It should return a MUMmerplot identical to the image provided. For reference I also included the corresponding log User manual ¶ dRep has 3 commands: compare, dereplicate, and check dependencies. Align whole genomes with nucmer; filter alignment; compare aligned regions ANIn = Align whole genomes with nucmer; compare aligned regions gANI = Identify and align ORFs; compare aligned ORFS goANI = Open source version of gANI; requires nsmimscan (default Supermap: find set of non-overlapping anchors in BLAST or NUCMER output. Longest or heaviest increasing subsequence. Matrix operations. apps. GenBank entrez accession, phytozome, ensembl and SRA downloader. Calculate (non)synonymous substitution rate between gene pairs. Basic phylogenetic tree construction using PHYLIP, PhyML, or RAxML, and Download ABACAS from the download page; Run: perl abacas.pl -r -q -p NOTE: If ABACAS cannot find MUMmer from the default path - it will prompt the user to enter the location of MUMer ABACAS may take several minutes to run for large genomes/chromosomes and will produce a number of different output files in the working directory The programs tblastx and promer have more detection power than blastn and nucmer, respectively, thereby allowing the detection of genomic sub-regions that share low sequence similarities. The user can also obtain a text-based alignment of any subregions using bl2seq, nucmer, promer, MAFFT, and ClustalW. Instructions. Upload a delta file to analyze alignments of an assembly to another assembly or a reference genome. $ nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT. Then use the OUT.delta.gz file for upload. Upload the .delta or delta.gz file ( view example) to Assemblyti